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RDAP 033111

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Philip Bourne
Philip Bourne

Presentation on the RCSB PDB at the 2nd Research Data Access and Preservation (RDAP) Summit Denver Colorado March 31, 2011

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A Few RDAP Thoughts Based on Experience with The RCSB Protein Data Bank www.rcsb.org Philip E. Bourne UCSD [email_address] 3/31/11 RDAP Summit 2011
Disclaimer ,[object Object],[object Object],3/31/11 RDAP Summit 2011
What is the Protein Data Bank (PDB)? ,[object Object],[object Object],[object Object],[object Object],[object Object],3/31/11
PDB Total Contents by Year Number of released entries Year 3/31/11
Why We Think We Are Successful? ,[object Object]
Metric of Success - A Research Tool for Influenza * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Structure Summary page activity for H1N1 Influenza related structures * 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir Jan. 2008 Jan. 2009 Jan. 2010 Jul. 2009 Jul. 2008 Jul. 2010 1RUZ: 1918 H1 Hemagglutinin
Looking Back Over the Past 12 Years – In General ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Looking Back Over the Past 12 Years – Infrastructure ,[object Object],[object Object],[object Object],[object Object],[object Object],3/31/11 RDAP Summit 2011 Bluhm et al. 2011 Quality Assurance doi: 10.1093/database/bar003
Looking Back Over the Past 12 Years – Data & Data Management ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],3/31/11 RDAP Summit 2011
Trends Today ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],3/31/11 RDAP Summit 2011
Website Performance Improvements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Literature Integration – The Dream ,[object Object],[object Object],[object Object],[object Object],1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle PLoS Comp. Biol. 2005 1(3) e34
Example of Interoperability: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220
Example of Interoperability – The Literature View From Anita de Waard, Elsevier
Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673
Semantic Tagging of Database Content in The Literature or Elsewhere http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp PLoS Comp. Biol. 6(2) e1000673 Semantic Tagging
PDBMobile ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Objective: PDB Data Access On-The-Go
PDBMobile ,[object Object],[object Object],[object Object],[object Object],Tight Integration with MyPDB
Future ,[object Object],[object Object],[object Object]
Acknowledgements Funding Agencies: NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB, NINDS, NIDDK 3/31/11 RDAP Summit 2011

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RDAP 033111

  • 1. A Few RDAP Thoughts Based on Experience with The RCSB Protein Data Bank www.rcsb.org Philip E. Bourne UCSD [email_address] 3/31/11 RDAP Summit 2011
  • 2.
  • 3.
  • 4. PDB Total Contents by Year Number of released entries Year 3/31/11
  • 5.
  • 6. Metric of Success - A Research Tool for Influenza * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Structure Summary page activity for H1N1 Influenza related structures * 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir Jan. 2008 Jan. 2009 Jan. 2010 Jul. 2009 Jul. 2008 Jul. 2010 1RUZ: 1918 H1 Hemagglutinin
  • 7.
  • 8.
  • 9.
  • 10.
  • 11.
  • 12.
  • 13. Example of Interoperability: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220
  • 14. Example of Interoperability – The Literature View From Anita de Waard, Elsevier
  • 15. Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673
  • 16. Semantic Tagging of Database Content in The Literature or Elsewhere http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp PLoS Comp. Biol. 6(2) e1000673 Semantic Tagging
  • 17.
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  • 20. Acknowledgements Funding Agencies: NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB, NINDS, NIDDK 3/31/11 RDAP Summit 2011